RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddA 21,609 sequences; 6,263,737 total letters Searching..................................................done Query= gi|255764477|ref|YP_003065232.2| dephospho-CoA kinase [Candidatus Liberibacter asiaticus str. psy62] (199 letters) >gnl|CDD|30195 cd02022, DPCK, Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.. Length = 179 Score = 154 bits (390), Expect = 2e-38 Identities = 70/181 (38%), Positives = 107/181 (59%), Gaps = 6/181 (3%) Query: 3 IIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYHY--EAVDIIKKTFPRSI--QNN 58 IIGLTG IG+GK+TVA+ LK+ IPVI +D I ++Y A+ I + F I ++ Sbjct: 1 IIGLTGGIGSGKSTVAKLLKELGIPVIDADKIAHEVYEPGGPALQAIVEAFGPDILLEDG 60 Query: 59 KVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEKRK 118 ++++ +L I+ P K + LE I HP++R ++ L + R EK+V D PLLFE Sbjct: 61 ELDRKKLGEIVFADPEKRKKLEAITHPLIRKEIEEQLAE--ARKEKVVVLDIPLLFETGL 118 Query: 119 EYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGTIE 178 E L D V+VV E Q ER++ R +EE ++ QM ++K +RAD+VI+ G++E Sbjct: 119 EKLVDRVIVVDAPPEIQIERLMKRDGLSEEEAEARIASQMPLEEKRARADFVIDNSGSLE 178 Query: 179 A 179 Sbjct: 179 E 179 >gnl|CDD|30586 COG0237, CoaE, Dephospho-CoA kinase [Coenzyme metabolism]. Length = 201 Score = 135 bits (340), Expect = 1e-32 Identities = 68/199 (34%), Positives = 112/199 (56%), Gaps = 7/199 (3%) Query: 1 MLIIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLY--HYEAVDIIKKTFPRSI--Q 56 MLIIGLTG IG+GK+TVA+ L + PVI +DD+ ++ EA+ I + F I + Sbjct: 2 MLIIGLTGGIGSGKSTVAKILAELGFPVIDADDVAREVVEPGGEALQEIAERFGLEILDE 61 Query: 57 NNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEK 116 + +++ +L + P LEKI+HP++R K ++ V + PLLFE Sbjct: 62 DGGLDRRKLREKVFNDPEARLKLEKILHPLIRAEIKVVIDGAR---SPYVVLEIPLLFEA 118 Query: 117 RKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGT 176 E FD V+VV E + ER++ R EE+ L+ Q + ++K++ AD VI+ +G+ Sbjct: 119 GGEKYFDKVIVVYAPPEIRLERLMKRDGLDEEDAEARLASQRDLEEKLALADVVIDNDGS 178 Query: 177 IEAIEKETQKMLKYILKIN 195 IE + ++ +K+LK +L + Sbjct: 179 IENLLEQIEKLLKELLGLV 197 >gnl|CDD|144640 pfam01121, CoaE, Dephospho-CoA kinase. This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction. Length = 179 Score = 121 bits (305), Expect = 2e-28 Identities = 52/180 (28%), Positives = 91/180 (50%), Gaps = 7/180 (3%) Query: 2 LIIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYH--YEAVDIIKKTFPRSI--QN 57 LI+GLTG IG+GK+TVA +P++ +D I ++ A+ I F I + Sbjct: 1 LIVGLTGGIGSGKSTVANLFADLGVPIVDADVIARQVVEPGSPALAAIVDHFGPDILLAD 60 Query: 58 NKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEKR 117 ++++ L ++ P + + L I+HP++R K L L+ V D PLLFE Sbjct: 61 GQLDRRALRELVFSDPEEKQWLNAILHPLIRREMFKQLAQLT---SPYVLLDVPLLFESG 117 Query: 118 KEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGTI 177 L V+VV E Q ER++ R + E I++ Q + +++++ AD V++ + + Sbjct: 118 LTKLCHRVLVVDAPVELQVERLMQRDGLSREQVQAIIAAQASREERLALADDVLDNDSGL 177 >gnl|CDD|38430 KOG3220, KOG3220, KOG3220, Similar to bacterial dephospho-CoA kinase [Coenzyme transport and metabolism]. Length = 225 Score = 119 bits (300), Expect = 5e-28 Identities = 68/198 (34%), Positives = 106/198 (53%), Gaps = 4/198 (2%) Query: 1 MLIIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYH--YEAVDIIKKTFPRSI--Q 56 MLI+GLTG I TGK+TV++ K IPVI +D + ++ A I + F I + Sbjct: 1 MLIVGLTGGIATGKSTVSQVFKALGIPVIDADVVAREVVEPGTPAYRRIVEAFGTEILLE 60 Query: 57 NNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEK 116 + ++N+ L + P K + L KI HP +R K + L RG +++ D PLLFE Sbjct: 61 DGEINRKVLGKRVFSDPKKRQALNKITHPAIRKEMFKEILKLLLRGYRVIVLDIPLLFEA 120 Query: 117 RKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADYVINTEGT 176 + + VVVTC E Q ER++ R + +EE+ L QM + K AD VI+ G+ Sbjct: 121 KLLKICHKTVVVTCDEELQLERLVERDELSEEDAENRLQSQMPLEKKCELADVVIDNNGS 180 Query: 177 IEAIEKETQKMLKYILKI 194 +E + ++ +K+L + K Sbjct: 181 LEDLYEQVEKVLALLQKS 198 >gnl|CDD|32119 COG1936, COG1936, Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]. Length = 180 Score = 36.4 bits (84), Expect = 0.005 Identities = 15/48 (31%), Positives = 28/48 (58%) Query: 3 IIGLTGSIGTGKTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKT 50 +I +TG+ G GKTTV + L++ VI +++ + Y D ++K+ Sbjct: 2 LIAITGTPGVGKTTVCKLLRELGYKVIELNELAKENGLYTEYDELRKS 49 >gnl|CDD|38518 KOG3308, KOG3308, KOG3308, Uncharacterized protein of the uridine kinase family [Nucleotide transport and metabolism]. Length = 225 Score = 33.8 bits (77), Expect = 0.029 Identities = 33/202 (16%), Positives = 76/202 (37%), Gaps = 16/202 (7%) Query: 2 LIIGLTGSIGTGKTTVAEFLKK--EKIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNK 59 LI+G++G +GKTT+A+ L + +I DD Y+ + I+ + + Sbjct: 5 LIVGISGCTNSGKTTLAKSLHRFFPGCSLIHQDDF------YKPENEIEVDYNNIDNWDL 58 Query: 60 VNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGE------KIVFFDTPLL 113 + + L+K L+ + + + + IV D ++ Sbjct: 59 LESLDMEKFLEKIATWLDSRHNAPEAREHLVSYANFEHYAQQFQIKAYKNHIVIIDGFMI 118 Query: 114 FE-KRKEYLFDAVVVVTCSFETQRERVLSRKKH-TEENFLFILSKQMNEKDKISRADYVI 171 + K + LFD ++++T +ET + R +R + ++ F + + A Sbjct: 119 YNYKPQVDLFDRIIMLTLDYETCKRRREARTYYPPDDTGYFDPVVWPHYEKNFEEARDRS 178 Query: 172 NTEGTIEAIEKETQKMLKYILK 193 + + +K+ + + Sbjct: 179 RHDSLFLNGDVSEEKLDDKVNE 200 >gnl|CDD|30917 COG0572, Udk, Uridine kinase [Nucleotide transport and metabolism]. Length = 218 Score = 32.1 bits (73), Expect = 0.11 Identities = 20/35 (57%), Positives = 23/35 (65%), Gaps = 4/35 (11%) Query: 3 IIGLTGSIGTGKTTVA----EFLKKEKIPVISSDD 33 IIG+ G G+GKTTVA E L EK+ VIS DD Sbjct: 10 IIGIAGGSGSGKTTVAKELSEQLGVEKVVVISLDD 44 >gnl|CDD|30196 cd02023, UMPK, Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.. Length = 198 Score = 31.7 bits (72), Expect = 0.15 Identities = 17/34 (50%), Positives = 21/34 (61%), Gaps = 4/34 (11%) Query: 3 IIGLTGSIGTGKTTVA----EFLKKEKIPVISSD 32 IIG+ G G+GKTTVA E L K+ +IS D Sbjct: 1 IIGIAGGSGSGKTTVAEEIIEQLGNPKVVIISQD 34 >gnl|CDD|143797 pfam00004, AAA, ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes. Length = 131 Score = 30.3 bits (69), Expect = 0.42 Identities = 19/49 (38%), Positives = 28/49 (57%), Gaps = 4/49 (8%) Query: 6 LTGSIGTGKTTVAEFLKKE-KIPV--ISSDDIVDKLYHYEAVDIIKKTF 51 L G GTGKTT+A+ + KE P IS ++V K Y E+ +++ F Sbjct: 3 LYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSK-YVGESEKRLRELF 50 >gnl|CDD|31270 COG1072, CoaA, Panthothenate kinase [Coenzyme metabolism]. Length = 283 Score = 29.8 bits (67), Expect = 0.45 Identities = 10/22 (45%), Positives = 14/22 (63%) Query: 2 LIIGLTGSIGTGKTTVAEFLKK 23 IIG+ GS+ GK+T A L+ Sbjct: 83 FIIGIAGSVAVGKSTTARILQA 104 >gnl|CDD|31617 COG1428, COG1428, Deoxynucleoside kinases [Nucleotide transport and metabolism]. Length = 216 Score = 29.8 bits (67), Expect = 0.53 Identities = 32/161 (19%), Positives = 61/161 (37%), Gaps = 20/161 (12%) Query: 1 MLIIGLTGSIGTGKTTVAEFLKKE-KIPVIS----SDDIVDKLYHYEAVDIIKKTFPRSI 55 ++I + G IG GK+T+A+ L + V + +D Y D + F + Sbjct: 4 AMVIVIEGMIGAGKSTLAQALAEHLGFKVFYELVEDNPFLDLFYE----DPERYAFL--L 57 Query: 56 QNNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFE 115 Q + R I + K IL++ + + K + + ++D L++ Sbjct: 58 QIYFLLN-RFKKIKKALSDKNNILDRSIFEDYFLFAKLNFAKGTLSPSEFKYYDD--LYD 114 Query: 116 KRKEYLF------DAVVVVTCSFETQRERVLSRKKHTEENF 150 E L D ++ + S ET R+ R + E + Sbjct: 115 NMLEELPYLPGRPDLLIYLDASLETLLRRIAKRGRPFEIDN 155 >gnl|CDD|30727 COG0378, HypB, Ni2+-binding GTPase involved in regulation of expression and maturation of urease and hydrogenase [Posttranslational modification, protein turnover, chaperones / Transcription]. Length = 202 Score = 29.4 bits (66), Expect = 0.60 Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 5/37 (13%) Query: 1 MLIIGLTGSIGTGKT-----TVAEFLKKEKIPVISSD 32 ML IG+ G G+GKT T+ + KI VI+ D Sbjct: 13 MLRIGVGGPPGSGKTALIEKTLRALKDEYKIAVITGD 49 >gnl|CDD|33714 COG3932, COG3932, Uncharacterized ABC-type transport system, permease components [General function prediction only]. Length = 209 Score = 29.4 bits (66), Expect = 0.66 Identities = 11/37 (29%), Positives = 19/37 (51%) Query: 52 PRSIQNNKVNKARLLGILQKSPAKLEILEKIVHPMVR 88 PR I + + + +L G L+ ++ LE I P +R Sbjct: 86 PRKILDKTIKRRKLQGTLRAGKPWVKRLEAIARPRLR 122 >gnl|CDD|146080 pfam03266, DUF265, Protein of unknown function, DUF265. Length = 168 Score = 29.5 bits (67), Expect = 0.67 Identities = 14/29 (48%), Positives = 16/29 (55%), Gaps = 4/29 (13%) Query: 4 IGLTGSIGTGKTT----VAEFLKKEKIPV 28 I +TG G GKTT V E LK E + V Sbjct: 2 IFITGPPGVGKTTLVKKVIELLKSEGVKV 30 >gnl|CDD|31047 COG0703, AroK, Shikimate kinase [Amino acid transport and metabolism]. Length = 172 Score = 29.4 bits (66), Expect = 0.68 Identities = 46/197 (23%), Positives = 77/197 (39%), Gaps = 45/197 (22%) Query: 4 IGLTGSIGTGKTTVAEFLKKE-KIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKVNK 62 I L G +G GK+T+ L K +P I +D I+K SI Sbjct: 5 IVLIGFMGAGKSTIGRALAKALNLPFIDTD------------QEIEKRTGMSIA------ 46 Query: 63 ARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDT---PLLFEKRKE 119 EI E+ R E ++L +L ++ T +L E+ + Sbjct: 47 --------------EIFEEEGEEGFRRLETEVLKELLEEDNAVI--ATGGGAVLSEENRN 90 Query: 120 YLFDAVVVV--TCSFETQRERVLSRKKH---TEENFLFILSKQMNEKDKISR--ADYVIN 172 L +VV FET ER+ +K E+ L + + E+ + R AD++I+ Sbjct: 91 LLKKRGIVVYLDAPFETLYERLQRDRKRPLLQTEDPREELEELLEERQPLYREVADFIID 150 Query: 173 TEGTIEAIEKETQKMLK 189 T+ E + +E + L+ Sbjct: 151 TDDRSEEVVEEILEALE 167 >gnl|CDD|30188 cd00464, SK, Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.. Length = 154 Score = 29.4 bits (66), Expect = 0.74 Identities = 40/181 (22%), Positives = 68/181 (37%), Gaps = 40/181 (22%) Query: 3 IIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKVN 61 I L G +G GKTTV L K +P + D ++I++ SI Sbjct: 1 NIVLIGMMGAGKTTVGRLLAKALGLPFVDLD------------ELIEQRAGMSIP----- 43 Query: 62 KARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFD--TPLLFEKRKE 119 EI + R E+++L L + ++ L E R+ Sbjct: 44 ---------------EIFAEEGEEGFRELEREVLLLLLTKENAVIATGGGAVLREENRRL 88 Query: 120 YLFDAVVV-VTCSFETQRERVLSRKKH--TEENFLFILSKQMNEKDKISR--ADYVINTE 174 L + +VV + S E ER+ K ++ L + + E++ + R AD I+T+ Sbjct: 89 LLENGIVVWLDASPEELLERLARDKTRPLLQDEDPERLRELLEEREPLYREVADLTIDTD 148 Query: 175 G 175 Sbjct: 149 E 149 >gnl|CDD|109538 pfam00485, PRK, Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain. Length = 196 Score = 29.3 bits (66), Expect = 0.74 Identities = 12/17 (70%), Positives = 13/17 (76%) Query: 3 IIGLTGSIGTGKTTVAE 19 IIG+ GS G GKTTVA Sbjct: 1 IIGVAGSSGAGKTTVAR 17 >gnl|CDD|73295 cd02019, NK, Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.. Length = 69 Score = 29.1 bits (65), Expect = 0.87 Identities = 11/22 (50%), Positives = 17/22 (77%) Query: 3 IIGLTGSIGTGKTTVAEFLKKE 24 II +TG G+GK+TVA+ L ++ Sbjct: 1 IIAITGGSGSGKSTVAKKLAEQ 22 >gnl|CDD|30197 cd02024, NRK1, Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.. Length = 187 Score = 29.1 bits (65), Expect = 0.91 Identities = 30/156 (19%), Positives = 59/156 (37%), Gaps = 19/156 (12%) Query: 3 IIGLTGSIGTGKTTVAEFLKK--EKIPVISSDD----------IVDKLYHYEAVD-IIKK 49 I+G++G +GKTT+A+ L++ VI DD + ++ ++ + + Sbjct: 1 IVGISGVTNSGKTTLAKLLQRILPNCCVIHQDDFFKPEDEIPVDENGFKQWDVLEALDME 60 Query: 50 TFPRSIQNNKVNKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGE-KIVFF 108 ++ + +S EK + ++ DL + I+ Sbjct: 61 AMMSTLDY--WRETGHFPKFLRSHGNENDPEK--EFIEDAQIEETKADLLGAEDLHILIV 116 Query: 109 DTPLLFE-KRKEYLFDAVVVVTCSFETQRERVLSRK 143 D LL+ K LFD + +ET + R +R Sbjct: 117 DGFLLYNYKPLVDLFDIRYFLRVPYETCKRRREART 152 >gnl|CDD|30194 cd02021, GntK, Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.. Length = 150 Score = 28.7 bits (64), Expect = 1.00 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 1/33 (3%) Query: 3 IIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDI 34 II + G G+GK+TV + L ++ P I DD+ Sbjct: 1 IIVVMGVSGSGKSTVGKALAERLGAPFIDGDDL 33 Score = 26.4 bits (58), Expect = 5.3 Identities = 9/37 (24%), Positives = 12/37 (32%) Query: 117 RKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFI 153 K VVV CS + R + R F+ Sbjct: 66 AKLASAGEGVVVACSALKRIYRDILRGGAANPRVRFV 102 >gnl|CDD|30189 cd01428, ADK, Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.. Length = 194 Score = 28.7 bits (64), Expect = 1.0 Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%) Query: 3 IIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDIVDK 37 I L G G+GK T AE L KK +P IS+ D++ + Sbjct: 1 RILLLGPPGSGKGTQAERLAKKYGLPHISTGDLLRE 36 >gnl|CDD|30198 cd02025, PanK, Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.. Length = 220 Score = 28.7 bits (64), Expect = 1.1 Identities = 16/61 (26%), Positives = 28/61 (45%), Gaps = 9/61 (14%) Query: 3 IIGLTGSIGTGKTTVAEFLK--------KEKIPVISSDDIVDKLYHYEAVDII-KKTFPR 53 IIG+ GS+ GK+T A L+ + +I++D + ++ +K FP Sbjct: 1 IIGIAGSVAVGKSTTARVLQALLSRWPDHPNVELITTDGFLYPNKELIERGLMDRKGFPE 60 Query: 54 S 54 S Sbjct: 61 S 61 >gnl|CDD|38557 KOG3347, KOG3347, KOG3347, Predicted nucleotide kinase/nuclear protein involved oxidative stress response [Nucleotide transport and metabolism]. Length = 176 Score = 28.7 bits (64), Expect = 1.2 Identities = 34/140 (24%), Positives = 52/140 (37%), Gaps = 37/140 (26%) Query: 4 IGLTGSIGTGKTTVAEFLKKE-KIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKVNK 62 I +TG+ GTGK+T+AE L ++ + I D+V + YE D K +++ Sbjct: 10 ILVTGTPGTGKSTLAERLAEKTGLEYIEISDLVKENNLYEGYDEEYKCH-------ILDE 62 Query: 63 ARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVFFDTPLLFEKRKEYLF 122 ++L L L G IV + F E F Sbjct: 63 DKVL--------------------------DELEPLMIEGGNIVDYHGCDFF---PERWF 93 Query: 123 DAVVVVTCSFETQRERVLSR 142 D VVV+ +R+ SR Sbjct: 94 DLVVVLRTPNSVLYDRLKSR 113 >gnl|CDD|30909 COG0563, Adk, Adenylate kinase and related kinases [Nucleotide transport and metabolism]. Length = 178 Score = 28.7 bits (64), Expect = 1.2 Identities = 14/34 (41%), Positives = 22/34 (64%), Gaps = 4/34 (11%) Query: 2 LIIGLTGSIGTGKTTVAEFL-KKEKIPVISSDDI 34 LI+G G+ GK+T+A+ L KK +P + + DI Sbjct: 4 LILGPPGA---GKSTLAKKLAKKLGLPHLDTGDI 34 >gnl|CDD|73011 cd03252, ABCC_Hemolysin, The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E. coli. The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane. HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB. This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport. Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.. Length = 237 Score = 28.3 bits (63), Expect = 1.3 Identities = 15/66 (22%), Positives = 35/66 (53%), Gaps = 10/66 (15%) Query: 3 IIGLTGSIGTGKTTVAEFLKKEKIP-----VISSDDI--VDKLYHYEAVDIIKKT---FP 52 ++G+ G G+GK+T+ + +++ +P ++ D+ D + V ++ + F Sbjct: 30 VVGIVGRSGSGKSTLTKLIQRFYVPENGRVLVDGHDLALADPAWLRRQVGVVLQENVLFN 89 Query: 53 RSIQNN 58 RSI++N Sbjct: 90 RSIRDN 95 >gnl|CDD|110029 pfam00998, RdRP_3, Viral RNA dependent RNA polymerase. This family includes viral RNA dependent RNA polymerase enzymes from hepatitis C virus and various plant viruses. Length = 485 Score = 28.3 bits (64), Expect = 1.4 Identities = 20/98 (20%), Positives = 28/98 (28%), Gaps = 20/98 (20%) Query: 14 KTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKT--FPRSIQNNKVNKARLLGILQK 71 K V PV D I+ E ++I K PR I Q Sbjct: 101 KIYVKALESLAVKPVQRRDAILKTFVKAEKINITAKPDPAPRVI--------------QP 146 Query: 72 SPAKLEILEKIVHPMVRMHEKKILHDL-SCRGEKIVFF 108 P + +E +R EK + + G V Sbjct: 147 RPPRY-NVE--PGRYLRPCEKMLYKAIDKAFGGPTVLK 181 >gnl|CDD|146562 pfam03990, DUF348, Domain of unknown function (DUF348). This domain normally occurs as tandem repeats; however it is found as a single copy in the S. cerevisiae DNA-binding nuclear protein YCR593. This protein is involved in sporulation part of the SET3C complex, which is required to repress early/middle sporulation genes during meiosis. The bacterial proteins are likely to be involved in a cell wall function as they are found in conjunction with the pfam07501 domain, which is involved in various cell surface processes. Length = 43 Score = 28.2 bits (64), Expect = 1.5 Identities = 7/30 (23%), Positives = 15/30 (50%) Query: 5 GLTGSIGTGKTTVAEFLKKEKIPVISSDDI 34 G ++ T +TV + L++ I + D + Sbjct: 8 GKEKTVWTTASTVGDLLEEAGITLGEEDKV 37 >gnl|CDD|177083 CHL00181, cbbX, CbbX; Provisional. Length = 287 Score = 27.8 bits (62), Expect = 2.0 Identities = 16/39 (41%), Positives = 22/39 (56%), Gaps = 10/39 (25%) Query: 7 TGSIGTGKTTVA----------EFLKKEKIPVISSDDIV 35 TGS GTGKTTVA ++KK + ++ DD+V Sbjct: 65 TGSPGTGKTTVALKMADILYKLGYIKKGHLLTVTRDDLV 103 >gnl|CDD|31299 COG1102, Cmk, Cytidylate kinase [Nucleotide transport and metabolism]. Length = 179 Score = 27.9 bits (62), Expect = 2.1 Identities = 12/34 (35%), Positives = 22/34 (64%), Gaps = 1/34 (2%) Query: 2 LIIGLTGSIGTGKTTVAEFLKKE-KIPVISSDDI 34 ++I ++G G+GKTTVA L + + ++S+ I Sbjct: 1 MVITISGLPGSGKTTVARELAEHLGLKLVSAGTI 34 >gnl|CDD|133254 cd00878, Arf_Arl, Arf (ADP-ribosylation factor)/Arl (Arf-like) small GTPases. Arf proteins are activators of phospholipase D isoforms. Unlike Ras proteins they lack cysteine residues at their C-termini and therefore are unlikely to be prenylated. Arfs are N-terminally myristoylated. Members of the Arf family are regulators of vesicle formation in intracellular traffic that interact reversibly with membranes of the secretory and endocytic compartments in a GTP-dependent manner. They depart from other small GTP-binding proteins by a unique structural device, interswitch toggle, that implements front-back communication from N-terminus to the nucleotide binding site. Arf-like (Arl) proteins are close relatives of the Arf, but only Arl1 has been shown to function in membrane traffic like the Arf proteins. Arl2 has an unrelated function in the folding of native tubulin, and Arl4 may function in the nucleus. Most other Arf family proteins are so far relatively poorly characterized. Thus, despite their significant sequence homologies, Arf family proteins may regulate unrelated functions. Length = 158 Score = 27.9 bits (63), Expect = 2.1 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 15/54 (27%) Query: 2 LIIGLTGSIGTGKTTVAEFLKKEK----IPVISSDDIVDKLYHYEAVDIIKKTF 51 LI+GL G+ GKTT+ LK + IP I ++ E V+ +F Sbjct: 3 LILGLDGA---GKTTILYKLKLGEVVTTIPTIG--------FNVETVEYKNVSF 45 >gnl|CDD|33963 COG4240, COG4240, Predicted kinase [General function prediction only]. Length = 300 Score = 27.7 bits (61), Expect = 2.3 Identities = 15/59 (25%), Positives = 32/59 (54%), Gaps = 9/59 (15%) Query: 2 LIIGLTGSIGTGKTTVAEFLKK-------EKIPVISSDDIVDKLYHYEAVDIIKKTFPR 53 LI+G++G G+GK+T++ + + E+ +S DD+ L H + + + ++ P Sbjct: 51 LIVGISGPQGSGKSTLSALIVRLLAAKGLERTATLSLDDLY--LTHADRLRLARQVNPL 107 >gnl|CDD|31113 COG0770, MurF, UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]. Length = 451 Score = 27.6 bits (61), Expect = 2.3 Identities = 10/20 (50%), Positives = 12/20 (60%), Gaps = 2/20 (10%) Query: 3 IIGLTGSIGTGKTTVAEFLK 22 +I +TGS GKTT E L Sbjct: 105 VIAITGS--NGKTTTKEMLA 122 >gnl|CDD|73290 cd01983, Fer4_NifH, The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.. Length = 99 Score = 27.8 bits (61), Expect = 2.4 Identities = 15/37 (40%), Positives = 19/37 (51%), Gaps = 4/37 (10%) Query: 3 IIGLTGSIGTGKTTV----AEFLKKEKIPVISSDDIV 35 +I +TG G GKTT+ A L K V+ DD V Sbjct: 1 VIVVTGKGGVGKTTLAANLAAALAKRGKRVLLIDDYV 37 >gnl|CDD|147298 pfam05041, Pecanex_C, Pecanex protein (C-terminus). This family consists of C terminal region of the pecanex protein homologues. The pecanex protein is a maternal-effect neurogenic gene found in Drosophila. Length = 232 Score = 27.5 bits (61), Expect = 2.6 Identities = 15/49 (30%), Positives = 27/49 (55%), Gaps = 5/49 (10%) Query: 73 PAKLEILEKIVHPMVRMHEKKILHD-LSCRGEKIVFFDTPLLFEKRKEY 120 A +++L K+V P VRM K+ D +C E + + +L++ +EY Sbjct: 64 FADMDLLHKVVAPAVRM-SLKLHQDHFTCPDE---YDEPAVLYDAIQEY 108 >gnl|CDD|111395 pfam02492, cobW, CobW/HypB/UreG, nucleotide-binding domain. This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans. Length = 174 Score = 27.6 bits (62), Expect = 2.6 Identities = 12/33 (36%), Positives = 18/33 (54%), Gaps = 5/33 (15%) Query: 2 LIIGLTGSIGTGKTT-----VAEFLKKEKIPVI 29 + LTG +G+GKTT + + + KI VI Sbjct: 1 PVTVLTGFLGSGKTTLLEHLLRDNREGLKIAVI 33 >gnl|CDD|72981 cd03222, ABC_RNaseL_inhibitor, The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids. RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family. Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft. RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%. The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.. Length = 177 Score = 27.3 bits (60), Expect = 2.9 Identities = 25/107 (23%), Positives = 46/107 (42%), Gaps = 9/107 (8%) Query: 3 IIGLTGSIGTGKTTVAEFLKKEKIPVISSD--DIVDKLYHYEAVDIIKKTFPRSIQNNKV 60 +IG+ G GTGKTT + L + IP +D D + +Y + +D+ R + Sbjct: 27 VIGIVGPNGTGKTTAVKILAGQLIPNGDNDEWDGITPVYKPQYIDLSGGELQRVAIAAAL 86 Query: 61 NKARLLGILQKSPAKLEILEKIVHPMVRMHEKKILHDLSCRGEKIVF 107 + + + A L+I + R++ + + LS G+K Sbjct: 87 LRNATFYLFDEPSAYLDIEQ-------RLNAARAIRRLSEEGKKTAL 126 >gnl|CDD|37321 KOG2110, KOG2110, KOG2110, Uncharacterized conserved protein, contains WD40 repeats [Function unknown]. Length = 391 Score = 27.2 bits (60), Expect = 3.0 Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 3/72 (4%) Query: 4 IGLTGSIGTGKTTVAEFLKKEKIPVISS--DDIVDKLYHYE-AVDIIKKTFPRSIQNNKV 60 S T ++ E L + I S K+ H++ I + FP SI ++ Sbjct: 36 FEKCFSKDTEGVSIVEMLFSSSLVAIVSIKQPRKLKVVHFKKKTTICEIFFPTSILAVRM 95 Query: 61 NKARLLGILQKS 72 N+ RL+ L++S Sbjct: 96 NRKRLVVCLEES 107 >gnl|CDD|109594 pfam00543, P-II, Nitrogen regulatory protein P-II. P-II modulates the activity of glutamine synthetase. Length = 102 Score = 27.1 bits (61), Expect = 3.1 Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 5/39 (12%) Query: 13 GKTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKTF 51 G EFL K KI ++ D+ VD E V+ I K Sbjct: 45 GAEYYVEFLPKVKIEIVVPDEDVD-----EVVEAIIKAA 78 >gnl|CDD|112137 pfam03308, ArgK, ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems. Length = 267 Score = 26.9 bits (60), Expect = 3.4 Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 6/37 (16%) Query: 2 LIIGLTGSIGTGKTTVAEFLKKE------KIPVISSD 32 +G+TG G GK+T+ E L E ++ V++ D Sbjct: 30 HRVGITGVPGAGKSTLIEALGMELRRRGHRVAVLAVD 66 >gnl|CDD|48516 cd02967, mauD, Methylamine utilization (mau) D family; mauD protein is the translation product of the mauD gene found in methylotrophic bacteria, which are able to use methylamine as a sole carbon source and a nitrogen source. mauD is an essential accessory protein for the biosynthesis of methylamine dehydrogenase (MADH), the enzyme that catalyzes the oxidation of methylamine and other primary amines. MADH possesses an alpha2beta2 subunit structure; the alpha subunit is also referred to as the large subunit. Each beta (small) subunit contains a tryptophan tryptophylquinone (TTQ) prosthetic group. Accessory proteins are essential for the proper transport of MADH to the periplasm, TTQ synthesis and the formation of several structural disulfide bonds. Bacterial mutants containing an insertion on the mauD gene were unable to grow on methylamine as a sole carbon source, were found to lack the MADH small subunit and had decreased amounts of the MADH large subunit.. Length = 114 Score = 27.2 bits (60), Expect = 3.5 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 2/59 (3%) Query: 123 DAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNEKDKISRADY--VINTEGTIEA 179 D + VV S + E KKH E F ++LS ++ ++S+ Y +++ G I A Sbjct: 52 DWLDVVLASDGEKAEHQRFLKKHGLEAFPYVLSAELGMAYQVSKLPYAVLLDEAGVIAA 110 >gnl|CDD|48378 cd03114, ArgK-like, The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.. Length = 148 Score = 27.1 bits (60), Expect = 3.6 Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 6/36 (16%) Query: 3 IIGLTGSIGTGKTTVAEFL------KKEKIPVISSD 32 +IG+TG G GK+T+ + L + +++ V++ D Sbjct: 1 VIGITGVPGAGKSTLIDALITALRARGKRVAVLAID 36 >gnl|CDD|31889 COG1703, ArgK, Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]. Length = 323 Score = 26.8 bits (59), Expect = 3.8 Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 6/37 (16%) Query: 2 LIIGLTGSIGTGKTTVAEFLKKE------KIPVISSD 32 +IG+TG G GK+T+ E L +E ++ V++ D Sbjct: 52 HVIGITGVPGAGKSTLIEALGRELRERGHRVAVLAVD 88 >gnl|CDD|48380 cd03116, MobB, Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.. Length = 159 Score = 26.7 bits (59), Expect = 3.9 Identities = 11/21 (52%), Positives = 14/21 (66%) Query: 1 MLIIGLTGSIGTGKTTVAEFL 21 M +IG G G+GKTT+ E L Sbjct: 1 MKVIGFVGYSGSGKTTLLEKL 21 >gnl|CDD|31438 COG1245, COG1245, Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]. Length = 591 Score = 26.7 bits (59), Expect = 4.5 Identities = 9/31 (29%), Positives = 16/31 (51%) Query: 3 IIGLTGSIGTGKTTVAEFLKKEKIPVISSDD 33 ++G+ G G GK+T + L E P + + Sbjct: 102 VVGILGPNGIGKSTALKILAGELKPNLGRYE 132 >gnl|CDD|30199 cd02026, PRK, Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.. Length = 273 Score = 26.8 bits (59), Expect = 4.6 Identities = 14/42 (33%), Positives = 19/42 (45%), Gaps = 9/42 (21%) Query: 3 IIGLTGSIGTGKTT----VAEFLKKEKIPVISSDDIVDKLYH 40 IIG+ G G GK+T + + + VI DD YH Sbjct: 1 IIGVAGDSGCGKSTFLRRLTSLFGSDLVTVICLDD-----YH 37 >gnl|CDD|146552 pfam03975, CheD, CheD. This chemotaxis protein stimulates methylation of MCP proteins. Length = 105 Score = 26.7 bits (60), Expect = 4.9 Identities = 8/14 (57%), Positives = 12/14 (85%) Query: 19 EFLKKEKIPVISSD 32 E+LKKE IP+++ D Sbjct: 64 EYLKKEGIPIVAED 77 >gnl|CDD|73297 cd02034, CooC, The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.. Length = 116 Score = 26.3 bits (58), Expect = 5.4 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 8/44 (18%) Query: 3 IIGLTGSIGTGKTTV----AEFLKKEKIPVISSD----DIVDKL 38 I +TG G GKTT+ A +L ++ PV++ D D+ ++L Sbjct: 1 KIAITGKGGVGKTTIAALLARYLAEKGKPVLAIDADPDDLPERL 44 >gnl|CDD|33845 COG4088, COG4088, Predicted nucleotide kinase [Nucleotide transport and metabolism]. Length = 261 Score = 26.5 bits (58), Expect = 5.7 Identities = 19/66 (28%), Positives = 28/66 (42%), Gaps = 8/66 (12%) Query: 1 MLIIGLTGSIGTGKTTVAEFLKKE------KIPVISSDDIVDKLYHYEAVDIIKKTFPRS 54 M +I LTG G+GKTT A+ L KE ++ + D + ++ I K R Sbjct: 1 MPLIILTGYPGSGKTTFAKELAKELRQEIWRVIHLEKDYLR--GILWDESLPILKEVYRE 58 Query: 55 IQNNKV 60 V Sbjct: 59 SFLKSV 64 >gnl|CDD|35960 KOG0741, KOG0741, KOG0741, AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]. Length = 744 Score = 26.5 bits (58), Expect = 5.8 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 5/50 (10%) Query: 6 LTGSIGTGKTTVAEFLKKEK----IPVISSDDIVDKLYHYEAVDIIKKTF 51 L G G+GKT +A + + +IS +D++ L IKK F Sbjct: 543 LEGPPGSGKTALAAKIALSSDFPFVKIISPEDMIG-LSESAKCAHIKKIF 591 >gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.. Length = 151 Score = 26.3 bits (58), Expect = 6.0 Identities = 10/19 (52%), Positives = 12/19 (63%) Query: 6 LTGSIGTGKTTVAEFLKKE 24 L G GTGKTT+A + E Sbjct: 24 LYGPPGTGKTTLARAIANE 42 >gnl|CDD|31949 COG1763, MobB, Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]. Length = 161 Score = 26.1 bits (57), Expect = 6.3 Identities = 9/19 (47%), Positives = 13/19 (68%) Query: 1 MLIIGLTGSIGTGKTTVAE 19 M I+G+ G +GKTT+ E Sbjct: 2 MKILGIVGYKNSGKTTLIE 20 >gnl|CDD|38729 KOG3520, KOG3520, KOG3520, Predicted guanine nucleotide exchange factor [Signal transduction mechanisms]. Length = 1167 Score = 26.1 bits (57), Expect = 6.3 Identities = 22/117 (18%), Positives = 48/117 (41%), Gaps = 15/117 (12%) Query: 57 NNKVNKARLLGILQKSPAKLEILEKIVHPMVR--MHEKKILHD--LSCRGEK-------I 105 K RL I ++ AK K + + +K++HD L+ + + + Sbjct: 582 KEAEKKQRLEEIQRRLDAKSLSKYKNGEEFRKLDLTRRKLIHDGPLTWKTARGKTKDVHV 641 Query: 106 VFFDTPLLF--EKRKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLFILSKQMNE 160 + L+ EK ++Y+F ++ + Q+ ++ R+ T+E F++S Sbjct: 642 LLLTDILVLLQEKDQKYIFKSLDKKSPVISLQK--LIVREVATDEKAFFLISMSDQG 696 >gnl|CDD|30191 cd01673, dNK, Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.. Length = 193 Score = 26.0 bits (57), Expect = 6.8 Identities = 9/23 (39%), Positives = 16/23 (69%) Query: 3 IIGLTGSIGTGKTTVAEFLKKEK 25 +I + G+IG GK+T+A+ L + Sbjct: 1 VIVVEGNIGAGKSTLAKELAEHL 23 >gnl|CDD|48440 cd01911, proteasome_alpha, proteasome alpha subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 different alpha and 10 different beta proteasome subunit genes while archaea have one of each.. Length = 209 Score = 26.2 bits (58), Expect = 6.8 Identities = 8/52 (15%), Positives = 20/52 (38%), Gaps = 5/52 (9%) Query: 9 SIGTGKTTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIKKTFPRSIQNNKV 60 +IG G FL+K ++ ++ + A+ +K+ + + Sbjct: 158 AIGKGSQEAKTFLEKRYKKDLTLEEAIK-----LALKALKEVLEEDKKAKNI 204 >gnl|CDD|133370 cd04170, EF-G_bact, Elongation factor G (EF-G) subfamily. Translocation is mediated by EF-G (also called translocase). The structure of EF-G closely resembles that of the complex between EF-Tu and tRNA. This is an example of molecular mimicry; a protein domain evolved so that it mimics the shape of a tRNA molecule. EF-G in the GTP form binds to the ribosome, primarily through the interaction of its EF-Tu-like domain with the 50S subunit. The binding of EF-G to the ribosome in this manner stimulates the GTPase activity of EF-G. On GTP hydrolysis, EF-G undergoes a conformational change that forces its arm deeper into the A site on the 30S subunit. To accommodate this domain, the peptidyl-tRNA in the A site moves to the P site, carrying the mRNA and the deacylated tRNA with it. The ribosome may be prepared for these rearrangements by the initial binding of EF-G as well. The dissociation of EF-G leaves the ribosome ready to accept the next aminoacyl-tRNA into the A site. This group contains only bacterial members. Length = 268 Score = 26.0 bits (58), Expect = 7.9 Identities = 10/16 (62%), Positives = 12/16 (75%) Query: 4 IGLTGSIGTGKTTVAE 19 I L G G+GKTT+AE Sbjct: 2 IALVGHSGSGKTTLAE 17 >gnl|CDD|133425 cd05197, GH4_glycoside_hydrolases, Glycoside Hydrases Family 4. Glycoside hydrolases cleave glycosidic bonds to release smaller sugars from oligo- or polysaccharides. Some bacteria simultaneously translocate and phosphorylate disaccharides via the phosphoenolpyruvate-dependent phosphotransferase system (PEP-PTS). After translocation, these phospho-disaccharides may be hydrolyzed by GH4 glycoside hydrolases. Other organisms (such as archaea and Thermotoga maritima) lack the PEP-PTS system, but have several enzymes normally associated with the PEP-PTS operon. GH4 family members include 6-phospho-beta-glucosidases, 6-phospho-alpha-glucosidases, alpha-glucosidases/alpha-glucuronidases (only from Thermotoga), and alpha-galactosidases. They require two cofactors, NAD+ and a divalent metal (Mn2+, Ni2+, Mg2+), for activity. Some also require reducing conditions. GH4 glycoside hydrolases are part of the NAD(P)-binding Rossmann fold superfamily, which includes a wide variety of protein families including the NAD(P)-binding domains of alcohol dehydrogenases, tyrosine-dependent oxidoreductases, glyceraldehyde-3-phosphate dehydrogenases, formate/glycerate dehydrogenases, siroheme synthases, 6-phosphogluconate dehydrogenases, aminoacid dehydrogenases, repressor rex, and NAD-binding potassium channel domains, among others. Length = 425 Score = 25.9 bits (57), Expect = 8.4 Identities = 22/100 (22%), Positives = 37/100 (37%), Gaps = 23/100 (23%) Query: 93 KILHDLSCRGEKIVFFDTPLLFEKRKEYLFDAVVVVTCSFETQRERVLSRKKHTEENFLF 152 K +L ++ +D E+R + + + + + F Sbjct: 22 KTPEEL--PISEVTLYDID---EERLDIILTIA------------KRYVEEVGADIKFE- 63 Query: 153 ILSKQMNEKDKISRADYVINT--EGTIEAIEKETQKMLKY 190 K M+ +D I AD+VIN G + EK+ Q LKY Sbjct: 64 ---KTMDLEDAIIDADFVINQFRVGGLTYREKDEQIPLKY 100 >gnl|CDD|32202 COG2019, AdkA, Archaeal adenylate kinase [Nucleotide transport and metabolism]. Length = 189 Score = 25.6 bits (56), Expect = 9.2 Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 2/36 (5%) Query: 1 MLIIGLTGSIGTGKTTVAEFLKKE--KIPVISSDDI 34 ++ +TG G GKTTV + KE K +++ D+ Sbjct: 4 RKVVVITGVPGVGKTTVLKIALKELVKHKIVNYGDL 39 >gnl|CDD|144174 pfam00481, PP2C, Protein phosphatase 2C. Protein phosphatase 2C is a Mn++ or Mg++ dependent protein serine/threonine phosphatase. Length = 253 Score = 25.8 bits (57), Expect = 9.3 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%) Query: 15 TTVAEFLKKEKIPVISSDDIVDKLYHYEAVDIIK----KTFPRSIQNNKVNKAR 64 T + + ++ +++SD + D L E VDI++ P V++A Sbjct: 192 VTSHKITESDEFLILASDGLWDVLSDQEVVDIVRSELSDGDPMEAAEKLVDEAI 245 >gnl|CDD|176519 cd08577, PI-PLCc_GDPD_SF_unchar3, Uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipaseand Glycerophosphodiester phosphodiesterases. This subfamily corresponds to a group of uncharacterized hypothetical proteins similar to the catalytic domains of Phosphoinositide-specific phospholipase C (PI-PLC), and glycerophosphodiester phosphodiesterases (GP-GDE), and also sphingomyelinases D (SMases D) and similar proteins. They hydrolyze the 3'-5' phosphodiester bonds in different substrates, utilizing a similar mechanism of general base and acid catalysis involving two conserved histidine residues. Length = 228 Score = 25.7 bits (57), Expect = 9.3 Identities = 8/31 (25%), Positives = 13/31 (41%) Query: 106 VFFDTPLLFEKRKEYLFDAVVVVTCSFETQR 136 +FFD L + E L +++ SF Sbjct: 141 IFFDGRLDEDLPDEQLARLSPMISASFAKFS 171 >gnl|CDD|33383 COG3583, COG3583, Uncharacterized protein conserved in bacteria [Function unknown]. Length = 309 Score = 25.7 bits (56), Expect = 9.6 Identities = 14/31 (45%), Positives = 19/31 (61%) Query: 5 GLTGSIGTGKTTVAEFLKKEKIPVISSDDIV 35 G ++ T TTVA+ LK EKIP+ SD + Sbjct: 160 GKVRTVWTTATTVADLLKAEKIPLGKSDRVN 190 Database: CddA Posted date: Feb 4, 2011 9:38 PM Number of letters in database: 6,263,737 Number of sequences in database: 21,609 Lambda K H 0.319 0.136 0.371 Gapped Lambda K H 0.267 0.0731 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21609 Number of Hits to DB: 2,331,093 Number of extensions: 123650 Number of successful extensions: 716 Number of sequences better than 10.0: 1 Number of HSP's gapped: 708 Number of HSP's successfully gapped: 127 Length of query: 199 Length of database: 6,263,737 Length adjustment: 89 Effective length of query: 110 Effective length of database: 4,340,536 Effective search space: 477458960 Effective search space used: 477458960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 55 (25.0 bits)